NF1 c.4375_4377del, p.(Glu1459del)

Reasoning

The NF1 ClinGen specification is present but contains no usable PM2 population-source restriction or threshold, so the supplied generic ACMG/ClinGen-SVI default applies. The variant is absent from gnomAD v2.1 and gnomAD v4.1; it is also absent from the available gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer checks. This supports an allele frequency of 0 in the reported datasets, below the supplied PM2 supporting threshold of <=0.0001. PM2 is met at supporting strength.

Rule

Generic PM2 supporting threshold: allele frequency <=0.0001; absence in the applicable population datasets satisfies this threshold.

Evidence considered

• The NF1 ClinGen specification was reviewed first, but it provides no usable PM2 population-source restriction or threshold.
• gnomAD v2.1 reports the variant as absent, including the available non-cancer check.
• gnomAD v4.1 reports the variant as absent, and the available gnomAD v3.1 non-cancer check also reports absence.
• The supplied PM2 threshold is allele frequency <=0.0001 at supporting strength, following the ClinGen SVI recommendation (ACMG/AMP source cited as PMID:25741868).

Sources

Reasoning

The NF1 variant NM_001042492.2:c.4375_4377del is a 3-bp in-frame deletion predicted and normalized as NP_001035957.1:p.(Glu1459del), removing exactly one amino acid without altering the reading frame. This is the protein-length-change mechanism specified by generic ACMG/AMP PM4. The NF1 ClinGen specification is present but contains no structured PM4 rule or usable gene-specific exception, so the generic rule applies. The consequence is transcript-relevant because the variant is mapped to NF1 transcript NM_001042492.2 and exon 33, with the corresponding protein change confirmed by sequence normalization.

Rule

generic_acmg_pm4_protein_length_change

Evidence considered

• Sequence normalization maps NM_001042492.2:c.4375_4377del to NP_001035957.1:p.(Glu1459del), a 3-bp in-frame deletion removing one amino acid.
• Variant Validator places the deletion in NF1 exon 33 and confirms the predicted protein consequence p.(Glu1459del).
• The retrieved NF1 ClinGen framework is incomplete and provides no structured PM4 rule, so the generic ACMG/AMP protein-length-change rule is used.

Sources

Reasoning

The available literature and ClinVar-linked summaries do not provide a case-control comparison, odds ratio, likelihood ratio, or statistically significant enrichment for the exact variant NM_001042492.2:c.4375_4377del. Several cohort papers discuss NF1 mutation spectra or phenotype groups, but the precomputed exact-variant checks found that c.4375_4377del/p.(Glu1459del) was not explicitly reported in the reviewed papers. Reports of multiple individuals or a pathogenic laboratory label alone do not establish PS4.

Rule

Generic ACMG/AMP PS4: case-control or equivalent statistically significant enrichment of the exact variant in affected individuals versus controls is required; recurrence or a laboratory classification alone is insufficient.

Evidence considered

• The NF1 specification was located, but its extracted criterion payload is empty and incomplete; no NF1-specific PS4 rule or numeric threshold was available, so generic ACMG/AMP PS4 principles were used.
• PMID:12807981 studied 474 unrelated subjects and reported the mutation spectrum, including that amino-acid deletions represented 2% of 142 distinct mutations, but did not report the exact variant or an affected-versus-control enrichment analysis for it.
• PMID:15060124 reported four other in-frame deletions in an NF1 cohort, not p.(Glu1459del), and did not provide an exact-variant case-control enrichment statistic.
• PMID:26962827 found no clear relationship between specific NF1 mutations and clinical phenotypes in its 32-patient cohort and did not report c.4375_4377del.
• PMID:31776437 provided group-level phenotype frequencies for mutation categories, including in-frame deletions/insertions, but did not report the exact variant or establish exact-variant enrichment.
• ClinVar contains ordinary non-expert submissions and a multiple-submitter pathogenic/likely pathogenic aggregate, but no exact-match expert-panel assertion; these labels do not establish PS4.

Still missing

• No exact-variant case-control cohort with affected and control counts or a validated enrichment statistic was identified.

Sources

Reasoning

PP5 is not met. The ClinVar record selected for this case is not an exact validated match to the submitted transcript description, has no expert-panel submissions, and contains only ordinary laboratory or non-expert assertions. The pathogenic/likely pathogenic aggregate and literature-linked laboratory submissions therefore cannot trigger PP5 under the required exact-variant expert-panel rule.

Rule

PP5 may be applied only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification; ordinary submissions, aggregate labels, and non-expert assertions are excluded.

Evidence considered

• The ClinVar variation selected was NM_001042492.3(NF1):c.4372GAA[1] (p.Glu1459del), not an exact validated match to NM_001042492.2:c.4375_4377del.
• The ClinVar submission audit reports exact_match false, expert_panel_submissions 0, usable_for_classification 0, and ordinary clinical-laboratory or literature-only submissions.
• Under the requested rule, only an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification can support PP5; that evidence is absent.

Sources

Reasoning

The NF1 ClinGen specification is present but contains no usable population-frequency threshold or source restriction for BA1, so the supplied generic ACMG/AMP default applies. The variant is absent from gnomAD v2.1 and gnomAD v4.1, including the available gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer checks; therefore its observed allele frequency is 0 in the reported datasets, which is far below the generic BA1 stand-alone threshold of >=0.05 from ACMG/AMP 2015 (PMID:25741868). BA1 is not met.

Rule

Generic BA1 stand-alone threshold: allele frequency >=0.05; absence from the available gnomAD datasets does not meet this threshold.

Evidence considered

• The NF1 ClinGen specification was reviewed first, but it provides no usable BA1 population threshold or dataset restriction.
• gnomAD v2.1 reports the variant as absent; the corresponding non-cancer check also reports absence.
• gnomAD v4.1 reports the variant as absent; the corresponding v3.1 non-cancer check also reports absence.
• The supplied generic ACMG/AMP BA1 threshold is an allele frequency >=0.05, attributed to ACMG/AMP 2015 (PMID:25741868).

Sources

Reasoning

The NF1 ClinGen specification is present but contains no usable BS1 population-frequency threshold or source restriction, so the supplied generic ACMG/AMP default applies. The variant is absent from gnomAD v2.1 and gnomAD v4.1, and is also absent from the available non-cancer subset checks; its observed allele frequency is therefore 0 in the reported datasets, below the generic BS1 threshold of >=0.01. BS1 is not met.

Rule

Generic BS1 strong threshold: allele frequency >=0.01; absence from the available gnomAD datasets does not meet this threshold.

Evidence considered

• The NF1 ClinGen specification was reviewed first, but it provides no usable BS1 population threshold or dataset restriction.
• gnomAD v2.1 and gnomAD v4.1 both report the variant as absent; the available non-cancer checks also report absence.
• The supplied generic BS1 threshold is an allele frequency >=0.01, identified as the generic SVI default with per-gene derivation preferred (Whiffin et al. 2017, PMID:28518168).

Sources

Reasoning

BP3 applies to an in-frame deletion in a repetitive region with no demonstrated functional impact. The variant is indeed an in-frame one-amino-acid deletion, but the available variant-specific ClinVar evidence describes it as occurring in a non-repeat region, which fails BP3's repeat-region prerequisite. The ClinVar record is a best available candidate for the normalized p.Glu1459del representation rather than a validated exact HGVS match, so this repeat-context conclusion is assigned moderate rather than high confidence. No NF1 VCEP-specific BP3 rule was retrieved; the generic ACMG/AMP rule therefore applies.

Rule

generic_acmg_bp3_requires_repetitive_region

Evidence considered

• ClinVar evidence for the normalized p.Glu1459del representation describes an in-frame deletion of one amino acid in a non-repeat region; the candidate record was not validated as an exact HGVS match.
• The retrieved NF1 ClinGen framework is incomplete and provides no structured BP3 rule, so the generic ACMG/AMP repeat-region requirement is used.

Sources

Reasoning

BP6 is not met. The available ClinVar record has no exact validated match and no expert-panel submissions; its ordinary submissions are pathogenic or likely pathogenic rather than benign or likely benign. Therefore, there is no exact-variant ClinVar expert-panel Benign or Likely benign classification that could support BP6.

Rule

BP6 may be applied only for an exact-variant ClinVar expert-panel Benign or Likely benign classification; ordinary submissions, aggregate labels, and non-expert assertions are excluded.

Evidence considered

• The ClinVar submission audit reports exact_match false and expert_panel_submissions 0.
• The recorded ordinary submissions classify the variant as Pathogenic or Likely pathogenic; no Benign or Likely benign expert-panel assertion is present.
• Under the requested rule, ordinary laboratory submissions, aggregate labels, and non-expert assertions cannot trigger BP6.

Sources

Reasoning

The available ClinVar submission text reports this variant representation as de novo in one individual with confirmed parentage and as apparently de novo in another, but the retrieved ClinVar candidate is explicitly not an exact match to NM_001042492.2:c.4375_4377del and no primary case report, parental genotypes, family history, or phenotype documentation was provided to verify the assertion. Therefore confirmed de novo evidence cannot be adjudicated as PS2 from the available record.

Rule

PS2 requires a confirmed de novo occurrence with confirmed parentage and no stronger alternative explanation; unverified or non-exact variant records are insufficient.

Evidence considered

• ClinVar submission-signal text states that the alteration was identified as de novo with confirmed parentage in one individual and apparently de novo in another.
• The retrieved ClinVar variation is labeled NM_001042492.3:c.4372GAA[1] (p.Glu1459del); the audit states exact_match=false, so the de novo assertion is not independently validated for the submitted NM_001042492.2:c.4375_4377del representation.
• The NF1 VCEP/ClinGen framework was found, but its retrieved rule payload contains no PS2-specific rule; generic ACMG/AMP PS2 logic was therefore used only as fallback.

Still missing

• Primary-source confirmation that the reported individual carried NM_001042492.2:c.4375_4377del or an explicitly equivalent HGVS representation.
• Documented testing of both parents establishing maternity and paternity and absence of the variant.
• Relevant phenotype and family-history information for the reported proband.

Sources

Reasoning

The NF1 ClinGen specification is present but contains no usable criterion-specific rules, so generic ACMG/AMP PS3 guidance applies. The reviewed literature documents NF1 mutation-spectrum studies using cDNA/RNA or sequencing methods, but none explicitly reports NM_001042492.2:c.4375_4377del (NP_001035957.1:p.(Glu1459del)) or provides a variant-specific validated functional assay, assay controls, or a measured loss-of-function effect. The available ClinVar candidate record is not an exact variant match and its reported in-silico/de novo signals are not functional assay evidence. Therefore PS3 cannot be assigned at any strength.

Evidence considered

• The NF1 ClinGen specification (Version 1.0) was reviewed first; its extracted criteria and rule payload are empty, so it provides no usable PS3-specific calibration.
• PMID:12807981 reports an NF1 cohort assessed with cDNA-SSCP/heteroduplex, genomic sequencing, and RNA-effect analysis, but the exact c.4375_4377del/p.(Glu1459del) variant was not reported and no variant-specific functional result is given.
• PMID:15060124 reports four different in-frame NF1 deletions identified by sequencing; c.4375_4377del/p.(Glu1459del) is not among them and no assay result for this variant is provided.
• PMID:26962827 and PMID:31776437 describe cohort-level NF1 molecular or cDNA analyses, but neither reports the exact variant or a variant-specific functional effect.
• The ClinVar record selected for this case is not an exact variant match; its de novo and in-silico statements do not constitute validated functional evidence for PS3.

Still missing

• A variant-specific functional study is needed, such as validated NF1 protein-function, cellular RAS-GAP, or transcript assay with appropriate controls and a defined disease-relevant readout.

Sources

Reasoning

The available ClinVar submission text includes an apparently de novo assertion without confirmed parentage, but the retrieved candidate record is explicitly not an exact match to NM_001042492.2:c.4375_4377del and no primary report supplies the proband, parental testing, or phenotype details needed to verify this occurrence. The assertion is therefore insufficient to adjudicate PM6.

Rule

PM6 requires a credible de novo occurrence without confirmed parentage; an unverified assertion tied to a non-exact record is insufficient.

Evidence considered

• ClinVar submission-signal text states that the alteration was apparently de novo in an individual, but gives no primary case details in the available record.
• The ClinVar audit records exact_match=false for the retrieved candidate variation, preventing direct attribution of the assertion to the submitted HGVS representation.
• The NF1 VCEP/ClinGen framework was found, but its retrieved rule payload contains no PM6-specific rule; generic ACMG/AMP PM6 logic was therefore used only as fallback.

Still missing

• Primary-source confirmation of the exact variant in the reported proband.
• Clarification of whether maternity and paternity were tested and whether both parents were negative.
• Proband phenotype and family-history documentation.

Sources

Reasoning

No documented affected relatives, cosegregating meioses, family structure, or variant-positive and variant-negative relatives are available for NM_001042492.2:c.4375_4377del. The reviewed literature extracts describe cohort-level NF1 testing or mutation distributions and do not report this exact variant or usable family segregation data.

Rule

PP1 requires segregation of the variant with disease in informative affected relatives and meioses; no such variant-specific data are available.

Evidence considered

• PMID:26962827 describes familial segregation analyses in a 32-patient NF1 cohort but does not report c.4375_4377del or p.(Glu1459del), so it supplies no variant-specific PP1 evidence.
• PMID:12807981 reports an NF1 mutation cohort and RNA-level analyses but does not report c.4375_4377del or p.(Glu1459del), so it supplies no variant-specific PP1 evidence.
• The NF1 VCEP/ClinGen framework was found, but its retrieved rule payload contains no PP1-specific rule; generic ACMG/AMP PP1 logic was therefore used only as fallback.

Still missing

• A pedigree with affected and unaffected relatives tested for the variant.
• The number of informative meioses and each relative's phenotype and genotype.
• Primary-source family segregation data for the exact variant.

Sources

Reasoning

PP4 requires a highly specific phenotype or a phenotype strongly associated with the disease. The available records identify NF1-related conditions in ClinVar submissions and provide general NF1 phenotype context, but they do not provide a clinical phenotype for the individual being assessed that is sufficiently specific to NF1, nor do the reviewed papers establish the exact variant in a phenotype-defined case. Variant-level ClinVar labels and general NF1 descriptions cannot substitute for patient-specific phenotype documentation.

Rule

Generic ACMG/AMP PP4: a highly specific phenotype or family history strongly associated with the disease is required; a gene-level label or nonspecific clinical context is insufficient.

Evidence considered

• The NF1 specification was located, but its extracted criterion payload is empty and incomplete; no NF1-specific PP4 rule was available.
• ClinVar condition labels include NF1-related disorder and neurofibromatosis type 1, but the record is not an individual clinical phenotype assessment and the selected variation is not an exact validated match.
• PMID:26962827 and PMID:31776437 describe NF1 cohorts and phenotype categories at group level, not a patient-specific phenotype for this case or an exact-variant phenotype association.

Still missing

• Patient-specific clinical features and fulfillment of NF1 diagnostic criteria were not supplied.
• No exact-variant report with a documented highly specific NF1 phenotype was identified.

Sources

Reasoning

No applicable NF1-specific BS2 rule was available in the governing specification, and the case population data report only that the variant is absent from gnomAD v2.1, gnomAD v4.1, and the available non-cancer subset checks. Absence does not demonstrate observation in healthy adults, homozygotes, or individuals with a disease inconsistent with NF1; no qualifying BS2 observation or penetrance analysis is provided. BS2 cannot be assessed from the available evidence.

Rule

BS2 requires qualifying observation in healthy adults, homozygotes, or individuals with a phenotype inconsistent with the disease; absence from population databases is not sufficient.

Evidence considered

• The NF1 ClinGen specification was reviewed first, but no usable BS2-specific rule was available.
• The variant is absent from gnomAD v2.1 and gnomAD v4.1, with absence also reported by the available non-cancer subset checks.
• No source documents observation of this variant in healthy individuals, homozygotes, or individuals with a phenotype inconsistent with NF1.

Still missing

• A qualifying observation of the variant in healthy adults, homozygotes, or individuals with a clearly incompatible phenotype is not available.

Sources

Reasoning

The NF1 ClinGen specification is present but contains no usable criterion-specific rules, so generic ACMG/AMP BS3 guidance applies. The reviewed evidence contains no variant-specific well-established functional assay demonstrating a normal NF1 effect for NM_001042492.2:c.4375_4377del (NP_001035957.1:p.(Glu1459del)); the available cohort studies either do not report this exact variant or provide only group-level mutation-spectrum and genotype-phenotype observations. No validated benign assay result, assay controls, or disease-relevant normal-function measurement is available. Therefore BS3 cannot be assigned at any strength.

Evidence considered

• The NF1 ClinGen specification (Version 1.0) was reviewed first; its extracted criteria and rule payload are empty, so it provides no usable BS3-specific calibration.
• The reviewed NF1 cohort studies do not report a normal-function assay for the exact p.(Glu1459del) variant and do not establish benign functional behavior for it.
• PMID:12807981, PMID:15060124, PMID:26962827, and PMID:31776437 provide cohort-level molecular or clinical observations, not a validated variant-specific assay demonstrating preserved NF1 function.

Still missing

• A variant-specific, disease-relevant functional assay with appropriate positive and normal-function controls is needed to evaluate BS3.

Sources

Reasoning

No tested unaffected relatives carrying NM_001042492.2:c.4375_4377del, no informative non-segregation events, and no family-level genotype-phenotype data are documented. The available cohort publications do not report this exact variant or provide family observations that could establish lack of segregation.

Rule

BS4 requires a credible affected family context in which the variant is absent from affected individuals or present in unaffected individuals in a way that contradicts expected segregation; no such data are available.

Evidence considered

• PMID:26962827 reports cohort-level familial segregation analyses but does not report c.4375_4377del or any unaffected carrier relevant to BS4.
• PMID:12807981 does not report c.4375_4377del or family-level non-segregation data relevant to BS4.
• The NF1 VCEP/ClinGen framework was found, but its retrieved rule payload contains no BS4-specific rule; generic ACMG/AMP BS4 logic was therefore used only as fallback.

Still missing

• Testing results for unaffected relatives who carry the exact variant.
• A pedigree and phenotype assessment sufficient to distinguish age-dependent nonpenetrance from true non-segregation.
• Primary-source family data establishing non-segregation.

Sources

Reasoning

BP2 requires variant-specific phasing evidence showing this variant in cis with a pathogenic variant or in trans with a pathogenic variant in a dominant disorder. The available case evidence reports no affected proband, second NF1 variant, parental testing, or cis/trans phase result for NM_001042492.2:c.4375_4377del, and the reviewed publications do not provide such data; therefore BP2 cannot be assessed.

Rule

BP2: requires variant-specific cis or trans observation with another pathogenic variant and adequate phasing

Evidence considered

• The governing NF1 framework specifies autosomal dominant inheritance.
• The case evidence identifies NM_001042492.2:c.4375_4377del as an in-frame deletion producing p.(Glu1459del), but provides no second pathogenic NF1 variant, affected-proband genotype, parental testing, or cis/trans phase information.
• The reviewed variant-focused literature extractions did not report this exact variant or any qualifying cis/trans allelic observation.

Still missing

• Variant-specific testing of the affected individual and any additional NF1 variant are needed to establish whether the variants are in cis or trans.
• Parental or other family testing is needed to determine phase and inheritance if a second NF1 variant is identified.

Sources

Reasoning

No evidence was identified that a different molecular etiology explains the relevant phenotype in a way that satisfies BP5. The available records contain no validated alternative pathogenic variant or disease-causing mechanism for an evaluated individual, and the general NF1 literature does not provide such case-specific evidence. No BP5 numeric rule or opposite-direction likelihood-ratio threshold was available in the incomplete NF1 specification, so no numeric comparison can be performed.

Rule

Generic ACMG/AMP BP5: consider only when an alternative molecular etiology explains the patient's phenotype; no applicable NF1-specific rule or threshold was available.

Evidence considered

• The extracted NF1 specification contains no criterion-level BP5 rule or threshold.
• The case evidence does not document a validated alternative molecular cause for a patient's phenotype; ClinVar submissions concern this variant and are not evidence of an alternative diagnosis.
• Because no BP5 governing threshold was available and no numeric value was supplied, an operator-specific inequality cannot be written or used.

Still missing

• A documented phenotype and a validated alternative molecular diagnosis would be needed to assess BP5.
• The incomplete NF1 specification does not expose a BP5 rule or threshold.

Sources